testthat::context("Test m/z annotation")
test_annotateVOC_and_isotope <- function(){
library(ptairData)
bacteria_dir.c <- system.file("extdata/mycobacteria", package = "ptairData")
bacteria.ptrset <- createPtrSet(bacteria_dir.c, setName = "bacteria",
mzCalibRef = c(21.022,59.049), fracMaxTIC = 0.8, saveDir = NULL)
bacteria.ptrset <- detectPeak(bacteria.ptrset, mzNominal = c(21,59,60))
bacteria.eset <- alignSamples(bacteria.ptrset,pValGreaterThres = 0.05,quanti="ppb",fracExp = 1)
# numeric vector
annotateVectorDF <- ptairMS::annotateVOC(as.numeric(Biobase::featureNames(bacteria.eset)))
testthat::expect_identical(annotateVectorDF[1, "vocDB_name_iupac"],
"prop-2-en-1-ol, propan-2-one, propanal")
# data.frame
fdataDF <- Biobase::fData(bacteria.eset)
annotateDataFrameDF <- annotateVOC(fdataDF)
testthat::expect_identical(annotateDataFrameDF[1, "vocDB_name_iupac"],
"prop-2-en-1-ol, propan-2-one, propanal")
# ExpressionSet
bacteria.eset <- annotateVOC(bacteria.eset)
testthat::expect_identical(Biobase::fData(bacteria.eset)[1, "vocDB_name_iupac"],
"prop-2-en-1-ol, propan-2-one, propanal")
bacteria.eset <-findIsotope(bacteria.eset)
testthat::expect_equal( Biobase::fData(bacteria.eset)[1,"isotope"],row.names(Biobase::fData(bacteria.eset))[2])
}
test_that("annotateVOC function and findIsotope",test_annotateVOC_and_isotope())
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